Improving Néel Domain Walls Dynamics and Skyrmion Stability Using He Ion Irradiation.

Ion irradiation with light ions is an appealing way to finely tune the magnetic properties of thin magnetic films and in particular the perpendicular magnetic anisotropy (PMA). In this work, the effect of He+ irradiation on the magnetization reversal and on the domain wall dynamics  of Pt/Co/AlOx trilayers is illustrated. Fluences up to 1.5 × 1015 ions cm-2 strongly decrease the PMA, without affecting neither the spontaneous magnetization nor the strength of the interfacial Dzyaloshinskii-Moriya interaction (DMI). This confirms experimentally the robustness of the DMI interaction against interfacial chemical intermixing, already predicted by theory. In parallel with the decrease of the PMA, a strong decrease of the domain wall depinning field is observed after irradiation. This allows the domain walls to reach large maximum velocities with a lower magnetic field compared to that needed for the pristine films. Decoupling PMA from DMI can, therefore, be beneficial for the design of low energy devices based on domain wall dynamics. When the samples are irradiated with larger He+ fluences, the magnetization gets close to the out-of-plane/in-plane reorientation transition, where ≈100nm size magnetic skyrmions are stabilized. It is observed that as the He+ fluence increases, the skyrmion size decreases while these magnetic textures become more stable against the application of an external magnetic field, as predicted by theoretical models developed for ultrathin films with labyrinthine domains.

Current-Driven Domain Wall Dynamics in Ferrimagnetic Nickel-Doped Mn4N Films: Very Large Domain Wall Velocities and Reversal of Motion Direction across the Magnetic Compensation Point.

Spin-transfer torque (STT) and spin-orbit torque (SOT) are spintronic phenomena allowing magnetization manipulation using electrical currents. Beyond their fundamental interest, they allow developing new classes of magnetic memories and logic devices, in particular based on domain wall (DW) motion. In this work, we report the study of STT-driven DW motion in ferrimagnetic manganese nickel nitride (Mn4-xNixN) films, in which magnetization and angular momentum compensation can be obtained by the fine adjustment of the Ni content. Large domain wall velocities, approaching 3000 m/s, are measured for Ni compositions close to the angular momentum compensation point. The reversal of the DW motion direction, observed when the compensation composition is crossed, is related to the change of direction of the angular momentum with respect to that of the spin polarization. This is confirmed by the results of ab initio band structure calculations.

Helium Ions Put Magnetic Skyrmions on the Track.

Magnetic skyrmions are deemed to be the forerunners of novel spintronic memory and logic devices. While their observation and their current-driven motion at room temperature have been demonstrated, certain issues regarding their nucleation, stability, pinning, and skyrmion Hall effect still need to be overcome to realize functional devices. Here, we demonstrate that focused He+-ion-irradiation can be used to create and guide skyrmions in racetracks. We show that the reduction of the perpendicular magnetic anisotropy and Dzyaloshinskii-Moriya interaction in the track defined by ion-irradiation leads to the formation of stable isolated skyrmions. Current-driven skyrmion motion experiments and simulations reveal that the skyrmions move along the irradiated track, resulting in the suppression of the skyrmion Hall effect, and that the maximum skyrmion velocity can be enhanced by tuning the magnetic properties. These results open up a new path to nucleate and guide magnetic skyrmions in racetrack devices.

Kinetics of Ion Migration in the Electric Field-Driven Manipulation of Magnetic Anisotropy of Pt/Co/Oxide Multilayers.

Magneto-ionics is a fast developing research field which opens the perspective of energy efficient magnetic devices, where the magnetization direction is controlled by an electric field which drives the migration of ionic species. In this work, the interfacial perpendicular magnetic anisotropy (PMA) of Pt/Co/oxide stacks covered by ZrO2 , acting as a ionic conductor, is tuned by a gate voltage at room temperature. A large variation of the PMA is obtained by modifying the oxidation of the cobalt layer through the migration of oxygen ions: the easy magnetization axis can be switched reversibly from in-plane, with under-oxidized Co, to in-plane, with over-oxidized Co, passing through an out-of-plane magnetization state. The switching time between the different magnetic states is limited by the ion drift velocity. This depends exponentially on the gate voltage, and is varied by over five orders of magnitude, from several minutes to a few ms. The variation of the PMA versus time during the application of the gate voltage can be modeled with a parabolic variation of the PMA and an exponential decrease of the Co oxidation rate. The possibility to explain the observed effect with a simple theoretical model opens the possibility to engineer materials with optimized properties.

Large Current Driven Domain Wall Mobility and Gate Tuning of Coercivity in Ferrimagnetic Mn4N Thin Films.

Spintronics, which is the basis of a low-power, beyond-CMOS technology for computational and memory devices, remains up to now entirely based on critical materials such as Co, heavy metals and rare-earths. Here, we show that Mn4N, a rare-earth free ferrimagnet made of abundant elements, is an exciting candidate for the development of sustainable spintronics devices. Mn4N thin films grown epitaxially on SrTiO3 substrates possess remarkable properties, such as a perpendicular magnetization, a very high extraordinary Hall angle (2%) and smooth domain walls at the millimeter scale. Moreover, domain walls can be moved at record speeds by spin-polarized currents, in absence of spin-orbit torques. This can be explained by the large efficiency of the adiabatic spin transfer torque, due to the conjunction of a reduced magnetization and a large spin polarization. Finally, we show that the application of gate voltages through the SrTiO3 substrates allows modulating the Mn4N coercive field with a large efficiency.

Previously reported placebo-response-associated variants do not predict patient outcomes in inflammatory disease Phase III trial placebo arms.

In clinical trials, a placebo response refers to improvement in disease symptoms arising from the psychological effect of receiving a treatment rather than the actual treatment under investigation. Previous research has reported genomic variation associated with the likelihood of observing a placebo response, but these studies have been limited in scope and have not been validated. Here, we analyzed whole-genome sequencing data from 784 patients undergoing placebo treatment in Phase III Asthma or Rheumatoid Arthritis trials to assess the impact of previously reported variation on patient outcomes in the placebo arms and to identify novel variants associated with the placebo response. Contrary to expectations based on previous reports, we did not observe any statistically significant associations between genomic variants and placebo treatment outcome. Our findings suggest that the biological origin of the placebo response is complex and likely to be variable between disease areas.

The zebrafish reference genome sequence and its relationship to the human genome.

Zebrafish have become a popular organism for the study of vertebrate gene function. The virtually transparent embryos of this species, and the ability to accelerate genetic studies by gene knockdown or overexpression, have led to the widespread use of zebrafish in the detailed investigation of vertebrate gene function and increasingly, the study of human genetic disease. However, for effective modelling of human genetic disease it is important to understand the extent to which zebrafish genes and gene structures are related to orthologous human genes. To examine this, we generated a high-quality sequence assembly of the zebrafish genome, made up of an overlapping set of completely sequenced large-insert clones that were ordered and oriented using a high-resolution high-density meiotic map. Detailed automatic and manual annotation provides evidence of more than 26,000 protein-coding genes, the largest gene set of any vertebrate so far sequenced. Comparison to the human reference genome shows that approximately 70% of human genes have at least one obvious zebrafish orthologue. In addition, the high quality of this genome assembly provides a clearer understanding of key genomic features such as a unique repeat content, a scarcity of pseudogenes, an enrichment of zebrafish-specific genes on chromosome 4 and chromosomal regions that influence sex determination.

Unraveling Dzyaloshinskii-Moriya Interaction and Chiral Nature of Graphene/Cobalt Interface.

A major challenge for future spintronics is to develop suitable spin transport channels with long spin lifetime and propagation length. Graphene can meet these requirements, even at room temperature. On the other side, taking advantage of the fast motion of chiral textures, that is, Néel-type domain walls and magnetic skyrmions, can satisfy the demands for high-density data storage, low power consumption, and high processing speed. We have engineered epitaxial structures where an epitaxial ferromagnetic Co layer is sandwiched between an epitaxial Pt(111) buffer grown in turn onto MgO(111) substrates and a graphene layer. We provide evidence of a graphene-induced enhancement of the perpendicular magnetic anisotropy up to 4 nm thick Co films and of the existence of chiral left-handed Néel-type domain walls stabilized by the effective Dzyaloshinskii-Moriya interaction (DMI) in the stack. The experiments show evidence of a sizable DMI at the gr/Co interface, which is described in terms of a conduction electron mediated Rashba-DMI mechanism and points opposite to the spin orbit coupling-induced DMI at the Co/Pt interface. In addition, the presence of graphene results in (i) a surfactant action for the Co growth, producing an intercalated, flat, highly perfect face-centered cubic film, pseudomorphic with Pt and (ii) an efficient protection from oxidation. The magnetic chiral texture is stable at room temperature and grown on insulating substrate. Our findings open new routes to control chiral spin structures using interfacial engineering in graphene-based systems for future spin-orbitronics devices fully integrated on oxide substrates.

Velocity Enhancement by Synchronization of Magnetic Domain Walls.

Magnetic domain walls are objects whose dynamics is inseparably connected to their structure. In this Letter, we investigate magnetic bilayers, which are engineered such that a coupled pair of domain walls, one in each layer, is stabilized by a cooperation of Dzyaloshinskii-Moriya interaction and flux-closing mechanism. The dipolar field mediating the interaction between the two domain walls links not only their position but also their structure. We show that this link has a direct impact on their magnetic-field-induced dynamics. We demonstrate that in such a system the coupling leads to an increased domain wall velocity with respect to single domain walls. Since the domain wall dynamics is observed in a precessional regime, the dynamics involves the synchronization between the two walls to preserve the flux closure during motion. Properties of these coupled oscillating walls can be tuned by an additional in-plane magnetic field enabling a rich variety of states, from perfect synchronization to complete detuning.

The Skyrmion Switch: Turning Magnetic Skyrmion Bubbles on and off with an Electric Field.

Nanoscale magnetic skyrmions are considered as potential information carriers for future spintronics memory and logic devices. Such applications will require the control of their local creation and annihilation, which involves so far solutions that are either energy consuming or difficult to integrate. Here we demonstrate the control of skyrmion bubbles nucleation and annihilation using electric field gating, an easily integrable and potentially energetically efficient solution. We present a detailed stability diagram of the skyrmion bubbles in a Pt/Co/oxide trilayer and show that their stability can be controlled via an applied electric field. An analytical bubble model with the Dzyaloshinskii-Moriya interaction imbedded in the domain wall energy accounts for the observed electrical skyrmion switching effect. This allows us to unveil the origin of the electrical control of skyrmions stability and to show that both magnetic dipolar interaction and the Dzyaloshinskii-Moriya interaction play an important role in the skyrmion bubble stabilization.

The genome sequence of Atlantic cod reveals a unique immune system.

Atlantic cod (Gadus morhua) is a large, cold-adapted teleost that sustains long-standing commercial fisheries and incipient aquaculture. Here we present the genome sequence of Atlantic cod, showing evidence for complex thermal adaptations in its haemoglobin gene cluster and an unusual immune architecture compared to other sequenced vertebrates. The genome assembly was obtained exclusively by 454 sequencing of shotgun and paired-end libraries, and automated annotation identified 22,154 genes. The major histocompatibility complex (MHC) II is a conserved feature of the adaptive immune system of jawed vertebrates, but we show that Atlantic cod has lost the genes for MHC II, CD4 and invariant chain (Ii) that are essential for the function of this pathway. Nevertheless, Atlantic cod is not exceptionally susceptible to disease under natural conditions. We find a highly expanded number of MHC I genes and a unique composition of its Toll-like receptor (TLR) families. This indicates how the Atlantic cod immune system has evolved compensatory mechanisms in both adaptive and innate immunity in the absence of MHC II. These observations affect fundamental assumptions about the evolution of the adaptive immune system and its components in vertebrates.

Combining RT-PCR-seq and RNA-seq to catalog all genic elements encoded in the human genome.

Within the ENCODE Consortium, GENCODE aimed to accurately annotate all protein-coding genes, pseudogenes, and noncoding transcribed loci in the human genome through manual curation and computational methods. Annotated transcript structures were assessed, and less well-supported loci were systematically, experimentally validated. Predicted exon-exon junctions were evaluated by RT-PCR amplification followed by highly multiplexed sequencing readout, a method we called RT-PCR-seq. Seventy-nine percent of all assessed junctions are confirmed by this evaluation procedure, demonstrating the high quality of the GENCODE gene set. RT-PCR-seq was also efficient to screen gene models predicted using the Human Body Map (HBM) RNA-seq data. We validated 73% of these predictions, thus confirming 1168 novel genes, mostly noncoding, which will further complement the GENCODE annotation. Our novel experimental validation pipeline is extremely sensitive, far more than unbiased transcriptome profiling through RNA sequencing, which is becoming the norm. For example, exon-exon junctions unique to GENCODE annotated transcripts are five times more likely to be corroborated with our targeted approach than with extensive large human transcriptome profiling. Data sets such as the HBM and ENCODE RNA-seq data fail sampling of low-expressed transcripts. Our RT-PCR-seq targeted approach also has the advantage of identifying novel exons of known genes, as we discovered unannotated exons in ~11% of assessed introns. We thus estimate that at least 18% of known loci have yet-unannotated exons. Our work demonstrates that the cataloging of all of the genic elements encoded in the human genome will necessitate a coordinated effort between unbiased and targeted approaches, like RNA-seq and RT-PCR-seq.

RNAcentral: A vision for an international database of RNA sequences.

During the last decade there has been a great increase in the number of noncoding RNA genes identified, including new classes such as microRNAs and piRNAs. There is also a large growth in the amount of experimental characterization of these RNA components. Despite this growth in information, it is still difficult for researchers to access RNA data, because key data resources for noncoding RNAs have not yet been created. The most pressing omission is the lack of a comprehensive RNA sequence database, much like UniProt, which provides a comprehensive set of protein knowledge. In this article we propose the creation of a new open public resource that we term RNAcentral, which will contain a comprehensive collection of RNA sequences and fill an important gap in the provision of biomedical databases. We envision RNA researchers from all over the world joining a federated RNAcentral network, contributing specialized knowledge and databases. RNAcentral would centralize key data that are currently held across a variety of databases, allowing researchers instant access to a single, unified resource. This resource would facilitate the next generation of RNA research and help drive further discoveries, including those that improve food production and human and animal health. We encourage additional RNA database resources and research groups to join this effort. We aim to obtain international network funding to further this endeavor.

Fast current-induced domain-wall motion controlled by the Rashba effect.

The propagation of magnetic domain walls induced by spin-polarized currents has launched new concepts for memory and logic devices. A wave of studies focusing on permalloy (NiFe) nanowires has found evidence for high domain-wall velocities (100 m s(-1); refs,), but has also exposed the drawbacks of this phenomenon for applications. Often the domain-wall displacements are not reproducible, their depinning from a thermally stable position is difficult and the domain-wall structural instability (Walker breakdown) limits the maximum velocity. Here, we show that the combined action of spin-transfer and spin-orbit torques offers a comprehensive solution to these problems. In an ultrathin Co nanowire, integrated in a trilayer with structural inversion asymmetry (SIA), the high spin-torque efficiency facilitates the depinning and leads to high mobility, while the SIA-mediated Rashba field controlling the domain-wall chirality stabilizes the Bloch domain-wall structure. Thus, the high-mobility regime is extended to higher current densities, allowing domain-wall velocities up to 400 m s(-1).

Ensembl's 10th year.

Ensembl (http://www.ensembl.org) integrates genomic information for a comprehensive set of chordate genomes with a particular focus on resources for human, mouse, rat, zebrafish and other high-value sequenced genomes. We provide complete gene annotations for all supported species in addition to specific resources that target genome variation, function and evolution. Ensembl data is accessible in a variety of formats including via our genome browser, API and BioMart. This year marks the tenth anniversary of Ensembl and in that time the project has grown with advances in genome technology. As of release 56 (September 2009), Ensembl supports 51 species including marmoset, pig, zebra finch, lizard, gorilla and wallaby, which were added in the past year. Major additions and improvements to Ensembl since our previous report include the incorporation of the human GRCh37 assembly, enhanced visualisation and data-mining options for the Ensembl regulatory features and continued development of our software infrastructure.

Fighting Acinetobacter baumannii infections with the acylase PvdQ.

Acinetobacter baumannii is an opportunistic Gram-negative bacterial pathogen that poses a threat for frail patients worldwide. The high ability to withstand environmental stresses as well as its resistance towards a broad range of antibiotics make A. baumannii an effective hard-to-eradicate pathogen. One of the key mechanisms mediating tolerance against antibiotic treatment is the formation of biofilms, a process that is controlled by a multitude of different regulatory mechanisms. A key factor with major impact on biofilm formation is cell-to-cell communication by quorum-sensing, which in A. baumannii is mediated by acyl homoserine lactone signaling molecules. Here we show that the Ntn-Hydrolase PvdQ from Pseudomonas aeruginosa can reduce biofilm formation by the A. baumannii ATCC 17978 type strain and several clinical isolates on abiotic surfaces. Further, our study shows that a combination treatment of PvdQ-mediated quorum-quenching with the antibiotic gentamicin has a synergistic effect on the clearance of A. baumannii biofilms and possible biofilm dispersal. Moreover, we demonstrate in a Galleria mellonella larval infection model that PvdQ administration significantly prolongs survival of the larvae. Altogether, we conclude that the acylase-mediated irreversible cleavage of quorum-sensing signaling molecules as exemplified with PvdQ can set a profound limit to the progression of A. baumannii infections.

Enzyme-Mediated Quenching of the Pseudomonas Quinolone Signal (PQS): A Comparison between Naturally Occurring and Engineered PQS-Cleaving Dioxygenases.

The opportunistic pathogen Pseudomonas aeruginosa employs quorum sensing to govern the production of many virulence factors. Interference with quorum sensing signaling has therefore been put forward as an attractive approach to disarm this pathogen. Here, we analyzed the quorum quenching properties of natural and engineered (2-alkyl-)3-hydroxy-4(1H)-quinolone 2,4-dioxygenases (HQDs) that inactivate the P. aeruginosa signal molecule PQS (Pseudomonas quinolone signal; 2-heptyl-3-hydroxy-4(1H)-quinolone). When added exogenously to P. aeruginosa cultures, all HQDs tested significantly reduced the levels of PQS and other alkylquinolone-type secondary metabolites deriving from the biosynthetic pathway, such as the respiratory inhibitor 2-heptyl-4-hydroxyquinoline N-oxide. HQDs from Nocardia farcinica and Streptomyces bingchenggensis, which combine low KM values for PQS with thermal stability and resilience in the presence of P. aeruginosa exoproducts, respectively, attenuated production of the virulence factors pyocyanin and pyoverdine. A delay in mortality was observed when Galleria mellonella larvae were infected with P. aeruginosa suspensions treated with the S. bingchenggensis HQD or with inhibitors of alkylquinolone biosynthesis. Our data indicate that quenching of PQS signaling has potential as an anti-virulence strategy; however, an efficient anti-virulence therapy against P. aeruginosa likely requires a combination of agents addressing multiple targets.

Discovery of chromene compounds as inhibitors of PvdQ acylase of Pseudomonas aeruginosa.

The acquisition of iron is a crucial mechanism for the survival of pathogenic bacteria such as Pseudomonas aeruginosa in eukaryotic hosts. The key iron chelator in this organism is the siderophore pyoverdine, which was shown to be crucial for iron homeostasis. Pyoverdine is a non-ribosomal peptide with several maturation steps in the cytoplasm and others in the periplasmatic space. A key enzyme for its maturation is the acylase PvdQ. The inhibition of PvdQ stops the maturation of pyoverdine causing a significant imbalance in the iron homeostasis and hence can negatively influence the survival of P. aeruginosa. In this work, we successfully synthesized chromene-derived inhibitory molecules targeting PvdQ in a low micromolar range. In silico modeling as well as kinetic evaluations of the inhibitors suggest a competitive inhibition of the PvdQ function. Further, we evaluated the inhibitor in vivo on P. aeruginosa cells and report a dose-dependent reduction of pyoverdine formation. The compound also showed a protecting effect in a Galleria mellonella infection model.

A whole genome sequencing study of moderate to severe asthma identifies a lung function locus associated with asthma risk.

Genome-wide association studies (GWAS) have identified many common variant loci associated with asthma susceptibility, but few studies investigate the genetics underlying moderate-to-severe asthma risk. Here, we present a whole-genome sequencing study comparing 3181 moderate-to-severe asthma patients to 3590 non-asthma controls. We demonstrate that asthma risk is genetically correlated with lung function measures and that this component of asthma risk is orthogonal to the eosinophil genetics that also contribute to disease susceptibility. We find that polygenic scores for reduced lung function are associated with younger asthma age of onset. Genome-wide, seven previously reported common asthma variant loci and one previously reported lung function locus, near THSD4, reach significance. We replicate association of the lung function locus in a recently published GWAS of moderate-to-severe asthma patients. We additionally replicate the association of a previously reported rare (minor allele frequency < 1%) coding variant in IL33 and show significant enrichment of rare variant burden in genes from common variant allergic disease loci. Our findings highlight the contribution of lung function genetics to moderate-to-severe asthma risk, and provide initial rare variant support for associations with moderate-to-severe asthma risk at several candidate genes from common variant loci.